He made a total of sixteen appearances during a three-month loan spell. Then in early November, Blackpool tried to sign him on a season-long loan deal, however, Everton blocked the move, preferring it to be made permanent.[8]

On 8 November Southern signed a two-and-a-half-year contract with the Seasiders for an undisclosed fee.[9] On 22 March 2003 he was injured five minutes into a 2–2 draw with Stockport County at Edgeley Park and missed the rest of the season.[10] He had an operation on his right knee in April,[11] then on 1 May he was named the Blackpool Gazette Player of the Year, jointly with Martin Bullock.[12]

He returned to action on 13 September in a 2–0 defeat to Bournemouth.[13] On 9 December in a Football League Trophy match against Stockport County, Southern collapsed midway through the second half and he needed keyhole surgery on his knee later that month which revealed he had a slight tear in the medial cartilage, which was removed.[14] He returned to action on 31 January 2004 as a 68th minute substitute in a 2–2 draw with Swindon Town at Bloomfield Road.[15] When Blackpool won the Football League Trophy at the Millennium Stadium in Cardiff on 21 March, Southern was left out of the squad by Steve McMahon, who chose his son, Stephen, ahead of him.[16]

"I have been totally out of favour ever since my gran's funeral before the cup final, he totally didn't want to know me really and he didn't want to play me. He must have his reasons, but I was as bewildered as everybody else. I didn't lose much sleep when I found out he was going, I was delighted to be honest, it is a fresh start for me in the summer."

—Southern in an interview on the club's official website, following McMahon's departure as manager in May.[17]

After scoring seven goals in the 2004–05 season, including both goals in a 2–1 win over Brentford on 22 March,[20] in April 2005 Southern signed a two-year extension to his contract with the Seasiders.[21]

Southern scored Blackpool's winning goal on 11 August 2007 in their first match back in the second tier of English football for 29 years as they beat Leicester City 1–0 at the Walkers Stadium on the opening day of the 2007–08 season.[26] On 1 December Southern suffered ankle ligament damage in a 1–0 win over Queens Park Rangers at Bloomfield Road, and had an operation later in the month.[27]

After suffering a knee injury which ruled him out of the first round of Premier League fixtures, upon his return Southern found himself being used as mainly as a substitute. He made his first start against his former club, Everton, on 6 November 2010.

During the first half of Blackpool's 2011–12 campaign, Southern was diagnosed with testicular cancer.[32] He was able to maintain his fitness during his treatment, and two months after his operation he returned to the side, as captain, on 28 January;[33] however, he had to leave the game before the hour mark after suffering a serious gash to his leg.

After 10 years at Bloomfield Road, it was reported by the Blackpool Gazette and Huddersfield Examiner that Huddersfield Town and Blackpool had sealed a deal, thought to be around the £300,000 mark, on 25 July 2012. The terms allowed Southern to play the first and last 15 minutes of his testimonial match against Everton on 5 August.[34] The transfer was confirmed by Huddersfield Town, the following day, as their sixth signing for the 2012–13 season.[35] Southern made his Huddersfield début in the League Cup first round 2–0 away defeat at Preston North End on 13 August 2012 playing the full 90 minutes.[36] He made his league début in the 1–0 defeat by Cardiff City at the Cardiff City Stadium on 17 August. He scored his first goal for the club in the 1–1 draw against Crystal Palace at Selhurst Park on 22 December. He was released by the club at the end of the 2013–14 season.[37]

a. 3 league play-off appearances for Blackpool in 2007 (included in 2006–07 total)
b. 3 league play-off appearances for Blackpool in 2010 (included in 2009–10 total)
c. 1 league play-off appearances for Blackpool in 2012 (included in 2011–12 total)
c. All Football League Trophy results are included in totals